Yum, tasty mutations...

mutation t@sting

 documentation

Prediction

disease causing

 Model: simple_aae, prob: 0.999995790094848 (classification due to ClinVar, real probability is shown anyway)      (explain)
Summary
  • amino acid sequence changed
  • known disease mutation at this position (HGMD CM960047)
  • known disease mutation at this position (HGMD CP015757)
  • known disease mutation: rs13673 (pathogenic)
  • protein features (might be) affected
  • splice site changes
 hyperlink
analysed issue analysis result
name of alteration no title
alteration (phys. location) chr1:21900274T>CN/A show variant in all transcripts   IGV
HGNC symbol ALPL
Ensembl transcript ID ENST00000539907
Genbank transcript ID NM_001177520
UniProt peptide P05186
alteration type single base exchange
alteration region CDS
DNA changes c.748T>C
cDNA.955T>C
g.64417T>C
AA changes F250L Score: 22 explain score(s)
position(s) of altered AA
if AA alteration in CDS		 250
frameshift no
known variant Reference ID: rs121918010
databasehomozygous (C/C)heterozygousallele carriers
1000G---
ExAC077

known disease mutation: rs13673 (pathogenic for Infantile hypophosphatasia|Adult hypophosphatasia|Hypophosphatasia|not provided) dbSNP  NCBI variation viewer
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)

known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)
known disease mutation at this position, please check HGMD for details (HGMD ID CM960047)
known disease mutation at this position, please check HGMD for details (HGMD ID CP015757)
regulatory features DNase1, Open Chromatin, DNase1 Hypersensitive Site
Gene Associated, Regulatory Feature, Gene associated regulatory feature
H3K27me3, Histone, Histone 3 Lysine 27 Tri-Methylation
H3K36me3, Histone, Histone 3 Lysine 36 Tri-Methylation
Non-Gene Associated, Regulatory Feature, Non-Gene associated regulatory feature
phyloP / phastCons
PhyloPPhastCons
(flanking)1.1261
4.061
(flanking)4.061
explain score(s) and/or inspect your position(s) in in UCSC Genome Browser
splice sites
effectgDNA positionscorewt detection sequence exon-intron border
Acc marginally increased64424wt: 0.4956 / mu: 0.5343 (marginal change - not scored)wt: GAACCCCAAAGGCTTCTTCTTGCTGGTGGAAGGTAGGGACC
mu: GAACCCCAAAGGCCTCTTCTTGCTGGTGGAAGGTAGGGACC		 tctt|GCTG
Donor increased64409wt: 0.21 / mu: 0.38wt: GAACCCCAAAGGCTT
mu: GAACCCCAAAGGCCT		 ACCC|caaa
Donor marginally increased64408wt: 0.9912 / mu: 0.9931 (marginal change - not scored)wt: AGAACCCCAAAGGCT
mu: AGAACCCCAAAGGCC		 AACC|ccaa
distance from splice site 19
Kozak consensus sequence altered? N/A
conservation
protein level for non-synonymous changes
speciesmatchgeneaaalignment
Human      250AIQILRKNPKGFFLLVEGGRIDHG
mutated  not conserved    250QILRKNPKGLFLLVEGGRIDH
Ptroglodytes  no homologue    
Mmulatta  all identical  ENSMMUG00000002217  327AIQILRKNPKGFFLLVEGGRIDH
Fcatus  all identical  ENSFCAG00000002960  327AIKILSKNPKGFFLLVEGGRIDH
Mmusculus  all identical  ENSMUSG00000028766  327ALRILTKNLKGFFLLVEGGRIDH
Ggallus  no homologue    
Trubripes  all identical  ENSTRUG00000004463  327KILKKNPNGFYLLVEGGRIDH
Drerio  all identical  ENSDARG00000015546  363AIKILKKNERGFFLLVEGGRIDH
Dmelanogaster  all conserved  FBgn0043791  360AMEILERQSAGRGYFLFVE
Celegans  no homologue    
Xtropicalis  no homologue    
protein features
start (aa)end (aa)featuredetails 
271271CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
303303CARBOHYDN-linked (GlcNAc...) (Potential).might get lost (downstream of altered splice site)
332332METALMagnesium (Potential).might get lost (downstream of altered splice site)
337337METALZinc 1 (Potential).might get lost (downstream of altered splice site)
341341METALZinc 1 (Potential).might get lost (downstream of altered splice site)
361361CONFLICTQ -> H (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
378378METALZinc 2 (Potential).might get lost (downstream of altered splice site)
379379METALZinc 2 (Potential).might get lost (downstream of altered splice site)
430430CARBOHYDN-linked (GlcNAc...).might get lost (downstream of altered splice site)
446446CONFLICTA -> P (in Ref. 1; BAA32129).might get lost (downstream of altered splice site)
454454METALZinc 1 (Potential).might get lost (downstream of altered splice site)
502502LIPIDGPI-anchor amidated serine (Probable).might get lost (downstream of altered splice site)
503524PROPEPRemoved in mature form (Probable). /FTId=PRO_0000024024.might get lost (downstream of altered splice site)
length of protein normal
AA sequence altered yes
position of stopcodon in wt / mu CDS 1344 / 1344
position (AA) of stopcodon in wt / mu AA sequence 448 / 448
position of stopcodon in wt / mu cDNA 1551 / 1551
poly(A) signal N/A
conservation
nucleotide level for all changes - no scoring up to now		 N/A
position of start ATG in wt / mu cDNA 208 / 208
chromosome 1
strand 1
last intron/exon boundary 1286
theoretical NMD boundary in CDS 1028
length of CDS 1344
coding sequence (CDS) position 748
cDNA position
(for ins/del: last normal base / first normal base)		 955
gDNA position
(for ins/del: last normal base / first normal base)		 64417
chromosomal position
(for ins/del: last normal base / first normal base)		 21900274
original gDNA sequence snippet TGCGGAAGAACCCCAAAGGCTTCTTCTTGCTGGTGGAAGGT
altered gDNA sequence snippet TGCGGAAGAACCCCAAAGGCCTCTTCTTGCTGGTGGAAGGT
original cDNA sequence snippet TGCGGAAGAACCCCAAAGGCTTCTTCTTGCTGGTGGAAGGA
altered cDNA sequence snippet TGCGGAAGAACCCCAAAGGCCTCTTCTTGCTGGTGGAAGGA
wildtype AA sequence MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGF FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
mutated AA sequence MPWSFRSSTP TWLRMSSCSW EMTYNTNAQV PDSAGTATAY LCGVKANEGT VGVSAATERS
RCNTTQGNEV TSILRWAKDA GKSVGIVTTT RVNHATPSAA YAHSADRDWY SDNEMPPEAL
SQGCKDIAYQ LMHNIRDIDV IMGGGRKYMY PKNKTDVEYE SDEKARGTRL DGLDLVDTWK
SFKPRYKHSH FIWNRTELLT LDPHNVDYLL GLFEPGDMQY ELNRNNVTDP SLSEMVVVAI
QILRKNPKGL FLLVEGGRID HGHHEGKAKQ ALHEAVEMDR AIGQAGSLTS SEDTLTVVTA
DHSHVFTFGG YTPRGNSIFG LAPMLSDTDK KPFTAILYGN GPGYKVVGGE RENVSMVDYA
HNNYQAQSAV PLRHETHGGE DVAVFSKGPM AHLLHGVHEQ NYVPHVMAYA ACIGANLGHC
APASSAGSLA AGPLLLALAL YPLSVLF*
speed 1.10 s
All positions are in basepairs (bp) if not explicitly stated differently.
AA/aa: amino acid; CDS: coding sequence; mu: mutated; NMD: nonsense-mediated mRNA decay; nt: nucleotide; wt: wildtype; TGP: 1000 Genomes Project